(Press-News.org) Investigators from the UCLA Health Jonsson Comprehensive Cancer Center have developed an artificial intelligence (AI) model based on epigenetic factors that is able to predict patient outcomes successfully across multiple cancer types.
The researchers found that by examining the gene expression patterns of epigenetic factors — factors that influence how genes are turned on or off — in tumors, they could categorize them into distinct groups to predict patient outcomes across various cancer types better than traditional measures like cancer grade and stage.
These findings, described in Communications Biology, also lay the groundwork for developing targeted therapies aimed at regulating epigenetic factors in cancer therapy, such as histone acetyltransferases and SWI/SNF chromatin remodelers.
“Traditionally, cancer has been viewed as primarily a result of genetic mutations within oncogenes or tumor suppressors,” said co-senior author Hilary Coller, professor of molecular, cell, and developmental biology and a member of the UCLA Health Jonsson Comprehensive Cancer Center and the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA. “However, the emergence of advanced next-generation sequencing technologies has made more people realize that the state of the chromatin and the levels of epigenetic factors that maintain this state are important for cancer and cancer progression. There are different aspects of the state of the chromatin — like whether the histone proteins are modified, or whether the nucleic acid bases of the DNA contain extra methyl groups — that can affect cancer outcomes. Understanding these differences between tumors could help us learn more about why some patients respond differently to treatments and why their outcomes vary.”
While previous studies have shown that mutations in the genes that encode epigenetic factors can affect an individual’s cancer susceptibility, little is known about how the levels of these factors impact cancer progression. This knowledge gap is crucial in fully understanding how epigenetics affects patient outcomes, noted Coller.
To see if there was a relationship between epigenetic patterns and clinical outcomes, the researchers analyzed the expression patterns of 720 epigenetic factors to classify tumors from 24 different cancer types into distinct clusters.
Out of the 24 adult cancer types, the team found that for 10 of the cancers, the clusters were associated with significant differences in patient outcomes, including progression-free survival, disease-specific survival, and overall survival.
This was especially true for adrenocortical carcinoma, kidney renal clear cell carcinoma, brain lower grade glioma, liver hepatocellular carcinoma and lung adenocarcinoma, where the differences were significant for all the survival measurements.
The clusters with poor outcomes tended to have higher cancer stage, larger tumor size, or more severe spread indicators.
“We saw that the prognostic efficacy of an epigenetic factor was dependent on the tissue-of-origin of the cancer type,” said Mithun Mitra, co-senior author of the study and an associate project scientist in the Coller laboratory. “We even saw this link in the few pediatric cancer types we analyzed. This may be helpful in deciding the cancer-specific relevance of therapeutically targeting these factors.”
The team then used epigenetic factor gene expression levels to train and test an AI model to predict patient outcomes. This model was specifically designed to predict what might happen for the five cancer types that had significant differences in survival measurements.
The scientists found the model could successfully divide patients with these five cancer types into two groups: one with a significantly higher chance of better outcomes and another with a higher chance of poorer outcomes.
They also saw that the genes that were most crucial for the AI model had a significant overlap with the cluster-defining signature genes.
“The pan-cancer AI model is trained and tested on the adult patients from the TCGA cohort and it would be good to test this on other independent datasets to explore its broad applicability,” said Mitra. “Similar epigenetic factor-based models could be generated for pediatric cancers to see what factors influence the decision-making process compared to the models built on adult cancers.”
“Our research helps provide a roadmap for similar AI models that can be generated through publicly-available lists of prognostic epigenetic factors,” said the study’s first author, Michael Cheng, a graduate student in the Bioinformatics Interdepartmental Program at UCLA. “The roadmap demonstrates how to identify certain influential factors in different types of cancer and contains exciting potential for predicting specific targets for cancer treatment.”
The study was funded in part by grants from the National Cancer Institute, Cancer Research Institute, Melanoma Research Alliance, Melanoma Research Foundation, National Institutes of Health and the UCLA Spore in Prostate Cancer.
END
Brigham researchers found an association between alterations in circadian rest-activity rhythms and risk of frailty incidence in older adults
Wearable devices can be used to measure a variety of signs and signals related to our health. A new study by researchers from Brigham and Women’s Hospital, a founding member of the Mass General Brigham healthcare system, suggests that such devices may also be able to help predict older adults at risk of health complications related to frailty. The team found an association between disturbances in daily patterns of rest and activity, or circadian ...
Threats posed by the climate crisis disproportionally affect certain communities and social groups that are more exposed. People living in low- and middle-income (LMIC) countries are at heightened risk. Within these countries, women typically face higher climate risk than men.
To show where women working in agri-food systems – systems that encompass production, but also post-harvest handling and distribution – are most threated by climate change, an international team of researchers has developed a hotspot map that identifies and ranks localities by threat level.
“We show that significant ...
Minimizing energy consumption is a fundamental element in our journey towards sustainable societies, and advanced materials play a key role in this regard. Carbon-fiber-reinforced plastics (CFRPs) and carbon-fiber-reinforced thermoplastics (CFRTPs) are two prominent examples of composite materials that can significantly improve energy efficiency in various fields of application.
These composites are made of carbon fibers embedded in a polymer matrix, such as epoxy resin. Thanks to their low weight and remarkable mechanical strength, CFRPs and CFRTPs can greatly ...
A research team led by Dr. Jae-woong Ko from the Department of Engineering Ceramics at the Korea Institute of Materials Science(KIMS) has succeeded in localizing silicon nitride bearing ball manufacturing technology for electric vehicle drive modules. KIMS is a government-funded research institute under the Ministry of Science and ICT. This achievement is significant because it overcomes the limitations of foreign dependence and opens up the possibility of domestic supply and demand.
Silicon nitride bearing ...
Infants prenatally exposed to cannabis are more likely to be born preterm, have a low birth weight, and require neonatal intensive care unit (NICU) care than infants without prenatal cannabis exposure, according to a study published today in the scientific journal Addiction. However, cannabis-exposed infants are not at greater risk of birth defects or death within one year, including sudden unexpected infant death.
First author Ms. Maryam Sorkhou comments, “The global increase in cannabis use among women of reproductive age also extends to pregnant women. ...
Research that could lead to the first early detection blood test for pancreatic cancer has received critical funding from PanKind, The Australian Pancreatic Cancer Foundation.
Pancreatic cancer is one of Australia’s biggest killers, with poor survival rates marred by a lack of distinct symptoms and screening tools needed to detect the disease in its initial stages.
It’s hoped the test will, for the first time, accurately identify patients with early stages of pancreatic cancer – a crucial step towards improving survival ...
A recent study published in Progress in Neurobiology and led by researchers at the University of Arizona College of Medicine – Tucson has developed an improved method to study Parkinson’s disease in the lab. Along the way, researchers also uncovered clues that may help scientists figure out how to detect Parkinson’s earlier and point the way toward better treatments.
Around a million Americans are living with Parkinson’s disease, a neurological disorder that causes difficulty in movement, balance and cognition. Symptoms worsen until tasks like ...
Warming has played a crucial role in various industrial and agricultural processes throughout history. Night-time warming, however, presents a distinct challenge due to the absence of solar radiation. During the night, direct radiative heat loss to outer space through the atmospheric transparent window (8-14 μm) can cause temperature to drop below freezing, posing significant threats to agriculture (crops), transportation (outdoor cables), and more.
Traditionally, achieving night-time warming ...
With the benefits of reducing time-cost and human efforts, automated testing has been widely used for quality assurance of mobile applications (apps). However, in complex interactive activities, manual testing can achieve higher coverage. However, the effectiveness of manual testing is highly dependent on the vital User Operation Process (UOP) of experienced testers.
To solve the problems, a research team led by Zhenyu CHEN and Chunrong FANG published their new research on 15 Oct 2023 in Frontiers of Computer Science co-published ...
CORVALLIS, Ore. – Oregon State University researchers have been awarded $2 million from the U.S. Department of Agriculture to develop improved ways of preventing stored potatoes from sprouting, particularly in the organic sector.
This research is pivotal given the rapid rise of the organic market in U.S. agriculture, the scientists note.
“The organic potato industry cannot depend on traditional chemical anti-sprouting treatments since synthetic chemicals are banned in certified organic,” said Valtcho Jeliazkov of OSU’s College of Agricultural ...
